Ammon Bundy, center, at the Malheur National Wildlife Refuge near Burns, Ore., during the occupation. (Rick Bowmer/Associated Press)

In a stunning loss for federal prosecutors, the leaders of a 41-day armed standoff at a national wildlife refuge in Oregon were acquitted of federal charges Thursday.

Brothers Ammon and Ryan Bundy and five others had been charged with conspiracy to prevent federal employees from doing their jobs by occupying the Malheur National Wildlife Refuge in Oregon’s sparsely populated high desert early this year.

A jury found them not guilty, setting off celebrations outside the federal courthouse in Portland. A man waved the American flag at passing traffic as someone blew a horn in celebration and a man trotted by on horseback while holding a flag.

"I think the jury saw through this and saw these were well-meaning, well-intentioned individuals," occupier David Fry's attorney, Per Olson, told reporters, according to a livefeed broadcast from outside the courthouse by the Oregonian newspaper. "They all came out here for a good purpose: because they cared."

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The defeat for the prosecution was especially unexpected because three of the seven defendants had chosen to represent themselves during the trial. Critics of the occupation said the verdict might embolden similar actions by right-wing anti-government groups in the future.

An incident broke out in the courtroom shortly after the verdict was announced. As Ammon Bundy's lawyer, Marcus Mumford, argued with the judge that his client should be released, he was surrounded by U.S. marshals and taken into custody, the Oregonian reported.

Mumford told reporters later that he had been tased, taken to a holding cell and would face charges. "They took me down on the ground, they rammed my head into the ground and they tased me," he said in a video posted to social media. "I was arrested, taken away, and I was cited."

The Malheur occupation began as a protest of the imprisonment of two Oregon ranchers who had been convicted of setting fire to federal land. The occupation eventually drew right-wing anti-government protesters from across the U.S. to protest the federal government's control of public land across the West.

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The occupation, which starkly divided members of the rural towns outside the refuge, was eventually ended after federal and state law enforcement arrested the protesters' leaders on a nearby highway. One of the occupiers, LaVoy Finicum, was shot and killed after he tried to escape law enforcement and reached for a gun, officials said.

"While we had hoped for a different outcome, we respect the verdict of the jury and thank them for their dedicated service during this long and difficult trial," Billy J. Williams, United States attorney for the District of Oregon, said in a statement after the verdict.

"For many weeks, hundreds of law enforcement officers — federal, state and local — worked around the clock to resolve the armed occupation at the Malheur National Wildlife Refuge peacefully. We believe now — as we did then — that protecting and defending this nation through rigorous obedience to the U.S. Constitution is our most important responsibility," said Greg Bretzing, special agent in charge of the FBI in Oregon.

The FBI and Oregon State Police traffic stop and shooting of Robert “LaVoy” Finicum in Oregon on Tuesday. Thevideo has been edited from the version released Thursday by the FBI. (Robert Meeks / Los Angeles Times)

"Although we are extremely disappointed in the verdict, we respect the court and the role of the jury in the American judicial system," Bretzing said.

Oregon Gov. Kate Brown said she was disappointed by the jury's decision.

"The occupation of the Malheur refuge by outsiders did not reflect the Oregon way of respectfully working together to resolve differences," Brown said. "I appreciate the due diligence of our federal partners and stand with the communities of Harney County and residents of Burns."

The acquittal is sure to rattle some residents of Harney County, where the refuge is located. County Judge Steve Grasty, the top elected official in Harney County and a frequent target of criticism by the Bundy brothers, declined to criticize the verdict in a brief interview Thursday.

"This nation has a great judicial system. It works. This one has run its course, and we have decision," Grasty said, adding, "I'm not trying to evade the issue, but I just haven't digested this."

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In addition to Ammon and Ryan Bundy, the other defendants were Shawna Cox, Jeff Banta, David Fry, Kenneth Medenbach and Neil Wampler.

During the trial, flag-waving supporters, some in boots and cowboy hats, marched around the courthouse, in part hoping jurors might see one of their signs stating "Google: jury nullification" — effectively urging jurors to acquit the defendants out of a belief that the law under which they are charged is wrong.

Ammon Bundy said he was trying to take over the refuge using a legal claim known as "adverse possession" — a method of gaining control of land by occupying it.

Ryan Bundy acted as his own attorney, and in his opening statement announced that he was "in favor of government as long as it's done correctly." He also submitted a copy of a pocket Constitution as a court exhibit.

Attorney Matthew Schindler, who assisted Medenbach, the only Oregon resident among the defendants, said his client's participation was, in part, an attempt to prevent the demise of rural life in America. "These people have no voice in Washington anymore," he said. As for the takeover, Schindler added, "It worked."

Federal prosecutors relied a great deal on evidence, including videotapes, that was provided by the defendants — the occupiers regularly filmed themselves during the standoff and held daily news briefings.

Ammon Bundy attended court in a suit but later resorted to wearing blue jail scrubs in protest. "Mr. Bundy," said his attorney, J. Morgan Philpot, "desires to appear as he is, a political prisoner not free to dress as if presumed innocent." Bundy also complained that he'd been "molested like an animal" at the county jail.

Angela Bundy, wife of Ryan Bundy, said she was "on pins and needles for a week" while the jury deliberated. She returned to their Nevada home, where the couple live with their eight children, to await a verdict. "We have been praying so hard," she said.

Her husband emailed her with the news Thursday.

"Oh, my goodness!" Angela Bundy said. "We are so excited. That judge tried really hard to keep the truth from coming out in that courtroom."

Bundy family members and other defendants still face federal charges in Nevada stemming from a 2014 armed standoff near the Bunkerville ranch owned by Cliven Bundy, the father of Ryan and Ammon Bundy. That standoff was connected with Cliven Bundy’s refusal to pay grazing fees to the federal government.

An environmental group opposed to the occupation, the Western Watersheds Project, called the verdict a disappointment.

People are going to get killed because of this verdict, because this jury has just given militias the green light to go after federal facilities with rifles.

Kieran Suckling, executive director of the Center for Biological Diversity

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"The failure to hold extremist militants accountable for their armed takeover of public property amplifies the risk to federal, state and local officials who are charged with the management of public property throughout the West," Executive Director Erik Molvar said in a statement.

"The sad result of this verdict is that it will now be necessary to increase the presence and patrols of law enforcement throughout our public lands in order to assure the safety of rangers, scientists and land managers who are required to travel to remote corners of the West in order to do their jobs," Molvar said.

Kieran Suckling, executive director of the Center for Biological Diversity, which helped rally birders and others in support of the refuge and its employees during the occupation, was in disbelief.

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"I just didn't think it was possible that 12 jurors could look at pictures of armed men taking over a federal facility and say that's not illegal," Suckling said in an interview. "This jury has just declared open season on federal facilities. People are going to get killed because of this verdict, because this jury has just given militias the green light to go after federal facilities with rifles."

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Suckling said threats and assaults against public-land employees had been on the rise.

"It's already an incredibly difficult, dangerous job," he said. "l feel frightened and worried for every public-land manager in America."

Times staff writers William Yardley in Seattle and Nigel Duara in Phoenix contributed to this report.